Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method (Q88031278)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27476956%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

title

Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method (English)

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20 March 2020

1

Nadine Homeyer

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20 March 2020

author name string

Holger Gohlke

series ordinal

2

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20 March 2020

publication date

10 January 2012

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20 March 2020

published in

Molecular Informatics

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20 March 2020

volume

31

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20 March 2020

issue

2

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20 March 2020

page(s)

114-122

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Protein-protein recognition and interaction hot spots in an antigen-antibody complex: free energy decomposition identifies "efficient amino acids".

20 March 2020

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Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?

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Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

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10 April 2023

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Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

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Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods

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Dual chaperone role of the C-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin

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Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

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Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties

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An improved method to predict the entropy term with the MM/PBSA approach.

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Cooperativity and specificity of Cys2His2 zinc finger protein-DNA interactions: a molecular dynamics simulation study.

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Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors

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Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity.

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Investigating the binding specificity of U1A-RNA by computational mutagenesis

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Rigorous Free Energy Calculations in Structure-Based Drug Design.

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10 April 2023

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A smooth particle mesh Ewald method

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Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

10 April 2023

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Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.

10 April 2023

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Analyzing the robustness of the MM/PBSA free energy calculation method: application to DNA conformational transitions.

10 April 2023

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10 April 2023

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Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance

10 April 2023

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Molecular mechanics methods for predicting protein-ligand binding.

10 April 2023

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Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design

10 April 2023

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Postprocessing of docked protein-ligand complexes using implicit solvation models.

10 April 2023

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Investigation of MM-PBSA rescoring of docking poses

10 April 2023

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10 April 2023

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Computational analysis of the binding affinities of the natural-product cyclopentapeptides argifin and argadin to chitinase B from Serratia marcescens

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10 April 2023

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Role of Water Molecules in Structure and Energetics of Pseudomonas aeruginosa Lectin I Interacting with Disaccharides

10 April 2023

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Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA.

10 April 2023

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10 April 2023

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10 April 2023

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High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing.

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Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction

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Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

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An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods

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Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

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1 reference

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10 April 2023

Identifiers

DOI

10.1002/MINF.201100135

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27476956%20AND%20SRC:MED&resulttype=core&format=json

20 March 2020

1 reference